MolNFT v1 · #27424 · protein
Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dttp-GDP complex
1XJE · Ribonucleotide reductase, B12-dependent: “Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dttp-GDP complex”. X-ray diffraction, 3 ligands (GDP, TTP, MG), 9 pockets (best druggability 0.76).…
- PDB
- 1XJE
- Type
- protein
- Length
- 1,245 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleotide reductase, B12-dependent
- EC
- 1.17.4.1
- UniProt
- O33839
- Ligands
- GDP, TTP, MG
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 627 | 46% helix, 14% strand | O33839 |
| B | Ribonucleotide reductase, B12-dependent (EC 1.17.4.1) | protein | 618 | 45% helix, 14% strand | O33839 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.76 | 0.80 | 112 | GDP |
| 2 | 822 | 0.74 | 0.79 | 100 | GDP |
| 3 | 140 | 0.64 | 0.86 | 23 | MG, TTP |
| 4 | 146 | 0.64 | 0.86 | 27 | TTP |
| 5 | 142 | 0.54 | 0.81 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1384 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1XJE · Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O33839
- Elsewhere: RCSB PDB 1XJE · PDBe 1XJE · UniProt O33839
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